Our previous research developed a novel tuberculosis (TB) DNA vaccine ag85a/b showed a significant therapeutic effect on the mouse tuberculosis model by intramuscular injection (IM) and electroporation (EP). However, the action mechanisms between these two vaccine immunization methods remain unclear. In a previous study, 96 M. tuberculosis (MTB) H37Rv-infected BALB/c mice were treated with PBS, 10μg, 50μg, 100μg, and 200μg ag85a/b DNA vaccine delivered by IM and EP three times at two-week intervals, respectively. In this study, peripheral blood mononuclear cells (PBMCs) from 3 mice in each group were isolated to extract total RNA. The gene expression profiles were analyzed using gene microarray technology to obtain differentially expressed (DE) genes. Finally, DE genes were validated by real-time reverse transcription-quantitive PCR (RT-qPCR) and the GEO database. After MTB infection, most of the up-regulated DE genes were related to the digestion and absorption of nutrients or neuroendocrine, for example, Iapp, Scg2, Chga, Amy2a5, etc, and most of the down-regulated DE genes were related to cellular structural and functional proteins, especially the structure and function proteins of alveolar epithelial cell, for example, Sftpc, Sftpd, Pdpn, etc. Most of the abnormally up-regulated or down-regulated DE genes in the TB model group were recovered in the 100μg and 200μg ag85a/b DNA IM groups and four DNA EP groups. The pancreatic secretion pathway down-regulated and Rap1 signal pathway up-regulated had particularly significant changes during the immunotherapy of the ag85a/b DNA vaccine on the mouse TB model. The action target and mechanism of IM and EP are highly consistent. Tuberculosis infection caused rapid catabolism and slow anabolism in mice. For the first time, we found that the effective dose of the ag85a/b DNA vaccine immunized whether by IM or EP could significantly up-regulate immune-related pathways and recover the metabolic disorder and the injury caused by MTB.